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Exclude initiative from boards

We recently started working with the Portfolio plug-in. With this we implemented a hierarchy Epic (new issue type project) -> Feature (Epic issue type) -> story.

The scrum teams are working from 1 project, in that project the teams have their own board. Items, on story level are tagged to a team, with that each team has its own backlog.

The newly added issue type for Epic to use and create roadmaps in portfolio ends up on the teams backlogs. When I change the teams backlog filter to exclude that issue type its also removed from the Portfolio plan.

How do I keep the Portfolio plan including the 3 levels but exclude the new issue type from the teams backlog?

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